Something I noticed and felt it should go in here.
I put in a "silent" index.php file into an /theme/mytheme/img/ directory of a theme and noticed that when I go via the Dashboard to edit said theme, WP picks it up as the Main Index. It didn't pick up the /theme/mytheme/index.php file and list it with the template.
I messed with the URL string to go to the right place but that made me go, HMMMM? I know I'm not the only one that protects directories using a silent php files but it left me wondering "what's up with that?"